knitr::opts_chunk$set(echo = FALSE,cache = TRUE)
library(xlsx)
library(ggplot2)
## Registered S3 methods overwritten by 'ggplot2':
## method from
## [.quosures rlang
## c.quosures rlang
## print.quosures rlang
library(gplots)
##
## Attaching package: 'gplots'
## The following object is masked from 'package:stats':
##
## lowess
library(gridExtra)
library(corrplot)
## corrplot 0.84 loaded
library(dplyr)
##
## Attaching package: 'dplyr'
## The following object is masked from 'package:gridExtra':
##
## combine
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(png)
library(grid)
library(heatmaply)
## Loading required package: plotly
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
## Loading required package: viridis
## Loading required package: viridisLite
## Registered S3 method overwritten by 'seriation':
## method from
## reorder.hclust gclus
##
## ======================
## Welcome to heatmaply version 0.16.0
##
## Type citation('heatmaply') for how to cite the package.
## Type ?heatmaply for the main documentation.
##
## The github page is: https://github.com/talgalili/heatmaply/
## Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
## Or contact: <tal.galili@gmail.com>
## ======================
## Warning: NAs introduced by coercion
## Tree.ID Allocation Column Row Rep. measure Height Flower Flower.Level
## 840 IN4E4 F1 2 20 N 7 M N 0
## 1363 IN4FM F1 3 17 N 11 H N 0
## Chl Flav Anth Height08 Height09
## 840 18.511 1.401 0.370 138 234
## 1363 59.122 1.640 0.483 166 245
## Warning: Factor `Height` contains implicit NA, consider using
## `forcats::fct_explicit_na`
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing missing values (geom_point).
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 21 rows containing non-finite values (stat_bin).
## Warning: Removed 21 rows containing non-finite values (stat_density).
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Tree.ID 158 0.26483 0.0016762 0.9733 0.5779
## Residuals 1631 2.80887 0.0017222
## [1] 0.08616099
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing missing values (geom_point).
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 21 rows containing non-finite values (stat_bin).
## Warning: Removed 21 rows containing non-finite values (stat_density).
## Analysis of Variance Table
##
## Response: F1$Chl5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Tree.ID 158 23815 150.73 0.6775 0.999
## Residuals 1631 362856 222.47
## [1] 0.06158903
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing missing values (geom_point).
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 21 rows containing non-finite values (stat_bin).
## Warning: Removed 21 rows containing non-finite values (stat_density).
## Analysis of Variance Table
##
## Response: F1$Flav5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Tree.ID 158 14.876 0.094149 1.8118 1.856e-08 ***
## Residuals 1631 84.754 0.051965
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.149308
## Warning: Removed 89 rows containing non-finite values (stat_boxplot).
## Warning: Removed 8 rows containing missing values (geom_point).
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 8 rows containing non-finite values (stat_bin).
## Warning: Removed 8 rows containing non-finite values (stat_density).
## Warning in anova.lm(mod181): ANOVA F-tests on an essentially perfect fit
## are unreliable
## Analysis of Variance Table
##
## Response: F1$H185
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Tree.ID 171 418774 2449 3.9594e+27 < 2.2e-16 ***
## Residuals 1550 0 0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 1
## Warning: Removed 90 rows containing non-finite values (stat_boxplot).
## Warning: Removed 9 rows containing missing values (geom_point).
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 9 rows containing non-finite values (stat_bin).
## Warning: Removed 9 rows containing non-finite values (stat_density).
## Warning in anova.lm(mod191): ANOVA F-tests on an essentially perfect fit
## are unreliable
## Analysis of Variance Table
##
## Response: F1$H195
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Tree.ID 170 429289 2525.2 3.72e+27 < 2.2e-16 ***
## Residuals 1550 0 0.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 1
## Warning: Removed 90 rows containing non-finite values (stat_boxplot).
## Warning: Removed 9 rows containing missing values (geom_point).
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 9 rows containing non-finite values (stat_bin).
## Warning: Removed 9 rows containing non-finite values (stat_density).
## Warning in anova.lm(modHD1): ANOVA F-tests on an essentially perfect fit
## are unreliable
## Analysis of Variance Table
##
## Response: F1$HDiff
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Tree.ID 170 382107 2247.7 6.3777e+27 < 2.2e-16 ***
## Residuals 1550 0 0.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 1
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Height 2 0.04916 0.0245811 14.523 5.537e-07 ***
## Residuals 1787 3.02454 0.0016925
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.0159945
## Analysis of Variance Table
##
## Response: F1$Chl5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Height 2 791 395.31 1.8307 0.1606
## Residuals 1787 385880 215.94
## [1] 0.002044692
## Analysis of Variance Table
##
## Response: F1$Flav5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Height 2 0.972 0.48589 8.8009 0.0001572 ***
## Residuals 1787 98.658 0.05521
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.009753874
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Row 49 0.00086 0.0000176 0.01 1
## Residuals 1740 3.07284 0.0017660
## [1] 0.000280517
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Analysis of Variance Table
##
## Response: F1$Chl5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Row 49 48 0.977 0.0044 1
## Residuals 1740 386623 222.197
## [1] 0.0001237819
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Analysis of Variance Table
##
## Response: F1$Flav5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Row 49 0.204 0.004166 0.0729 1
## Residuals 1740 99.426 0.057141
## [1] 0.002048742
## Warning: Removed 89 rows containing non-finite values (stat_boxplot).
## Analysis of Variance Table
##
## Response: F1$H185
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Row 49 24288 495.68 2.1009 1.659e-05 ***
## Residuals 1672 394486 235.94
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.05799867
## Warning: Removed 90 rows containing non-finite values (stat_boxplot).
## Analysis of Variance Table
##
## Response: F1$H195
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Row 49 36836 751.76 3.2009 1.777e-12 ***
## Residuals 1671 392453 234.86
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.08580726
## Warning: Removed 90 rows containing non-finite values (stat_boxplot).
## Analysis of Variance Table
##
## Response: F1$HDiff
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Row 49 2266 46.25 0.2035 1
## Residuals 1671 379841 227.31
+R.squared
## [1] 0.00593089
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Column 3 0.00038 0.00012737 0.074 0.9739
## Residuals 1786 3.07332 0.00172078
## [1] 0.0001243198
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$Chl5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Column 3 198 65.844 0.3043 0.8223
## Residuals 1786 386473 216.390
## [1] 0.0005108494
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$Flav5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Column 3 0.012 0.004060 0.0728 0.9746
## Residuals 1786 99.618 0.055777
## [1] 0.0001222632
## Warning: Removed 89 rows containing non-finite values (stat_boxplot).
## Warning: Removed 89 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$H185
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Column 3 15817 5272.4 22.479 2.826e-14 ***
## Residuals 1718 402957 234.6
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.03776989
## Warning: Removed 90 rows containing non-finite values (stat_boxplot).
## Warning: Removed 90 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$H195
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Column 3 23664 7887.8 33.389 < 2.2e-16 ***
## Residuals 1717 405626 236.2
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.05512251
## Warning: Removed 90 rows containing non-finite values (stat_boxplot).
## Warning: Removed 90 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$HDiff
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Column 3 1958 652.75 2.9483 0.03172 *
## Residuals 1717 380149 221.40
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.005124903
Flowering refers to presence or not of flowers, Flower Level refers to a measure relating to the number of flowers present (0 = no flowers, 1 = 1-10, 2 = 10-20, 3 = 20+)
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower.Level 3 0.0028 0.00093363 0.543 0.6529
## Residuals 1786 3.0709 0.00171943
## [1] 0.0009112453
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing non-finite values (stat_summary).
ANOVA Flowering Presence
R.squared Flowering Presence
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower 1 0.00039 0.00039351 0.2289 0.6324
## Residuals 1788 3.07330 0.00171885
## [1] 0.0001280242
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$Chl5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower.Level 3 1461 487.00 2.2579 0.07985 .
## Residuals 1786 385210 215.68
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.003778413
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$Chl5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower 1 19 18.847 0.0872 0.7679
## Residuals 1788 386652 216.248
## [1] 4.87422e-05
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$Flav5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower.Level 3 0.574 0.191220 3.4477 0.01606 *
## Residuals 1786 99.056 0.055463
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.005757915
## Warning: Removed 21 rows containing non-finite values (stat_boxplot).
## Warning: Removed 21 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$Flav5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower 1 0.24 0.240050 4.3184 0.03784 *
## Residuals 1788 99.39 0.055587
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.002409418
## Warning: Removed 89 rows containing non-finite values (stat_boxplot).
## Warning: Removed 89 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$H185
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower.Level 3 11639 3879.6 16.371 1.718e-10 ***
## Residuals 1718 407135 237.0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.02779275
## Warning: Removed 89 rows containing non-finite values (stat_boxplot).
## Warning: Removed 89 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$H185
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower 1 2126 2125.89 8.776 0.003094 **
## Residuals 1720 416648 242.24
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.005076449
## Warning: Removed 90 rows containing non-finite values (stat_boxplot).
## Warning: Removed 90 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$H195
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower.Level 3 8766 2922.09 11.931 9.858e-08 ***
## Residuals 1717 420523 244.92
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.02042042
## Warning: Removed 89 rows containing non-finite values (stat_boxplot).
## Warning: Removed 89 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$H195
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower 1 343 342.61 1.373 0.2415
## Residuals 1719 428947 249.53
## [1] 0.0007980757
## Warning: Removed 90 rows containing non-finite values (stat_boxplot).
## Warning: Removed 90 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$HDiff
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower.Level 3 11680 3893.3 18.046 1.569e-11 ***
## Residuals 1717 370428 215.7
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.0305669
## Warning: Removed 90 rows containing non-finite values (stat_boxplot).
## Warning: Removed 90 rows containing non-finite values (stat_summary).
## Analysis of Variance Table
##
## Response: F1$HDiff
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flower 1 4246 4245.9 19.316 1.176e-05 ***
## Residuals 1719 377862 219.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.01111171
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 21 rows containing non-finite values (stat_smooth).
## Warning: Removed 21 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Chl5 1 0.33366 0.33366 217.73 < 2.2e-16 ***
## Residuals 1788 2.74003 0.00153
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.1085545
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 21 rows containing non-finite values (stat_smooth).
## Warning: Removed 21 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flav5 1 0.08082 0.080820 48.283 5.148e-12 ***
## Residuals 1788 2.99288 0.001674
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.02629407
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 110 rows containing non-finite values (stat_smooth).
## Warning: Removed 110 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$H185 1 0.00199 0.0019900 1.1487 0.284
## Residuals 1699 2.94338 0.0017324
## [1] 0.0006756401
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 110 rows containing non-finite values (stat_smooth).
## Warning: Removed 110 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$H195 1 0.0000 0.00000073 4e-04 0.9836
## Residuals 1699 2.9454 0.00173359
## [1] 2.490926e-07
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 110 rows containing non-finite values (stat_smooth).
## Warning: Removed 110 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$HDiff 1 0.00209 0.0020945 1.2091 0.2717
## Residuals 1699 2.94327 0.0017324
## [1] 0.0007111262
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 21 rows containing non-finite values (stat_smooth).
## Warning: Removed 21 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Anth5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$Flav5 1 0.08082 0.080820 48.283 5.148e-12 ***
## Residuals 1788 2.99288 0.001674
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.02629407
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 110 rows containing non-finite values (stat_smooth).
## Warning: Removed 110 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Chl5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$H185 1 414 413.56 1.9052 0.1677
## Residuals 1699 368794 217.07
## [1] 0.001120119
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 110 rows containing non-finite values (stat_smooth).
## Warning: Removed 110 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Chl5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$H195 1 78 78.221 0.36 0.5486
## Residuals 1699 369130 217.263
## [1] 0.0002118618
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 110 rows containing non-finite values (stat_smooth).
## Warning: Removed 110 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Chl5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$HDiff 1 142 141.85 0.653 0.4191
## Residuals 1699 369066 217.22
## [1] 0.0003842085
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 110 rows containing non-finite values (stat_smooth).
## Warning: Removed 110 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Flav5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$H185 1 0.073 0.073328 1.3145 0.2517
## Residuals 1699 94.773 0.055782
## [1] 0.0007731187
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 110 rows containing non-finite values (stat_smooth).
## Warning: Removed 110 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Flav5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$H195 1 0.205 0.204977 3.6797 0.05525 .
## Residuals 1699 94.642 0.055704
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.002161139
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 110 rows containing non-finite values (stat_smooth).
## Warning: Removed 110 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$Flav5
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$HDiff 1 0.582 0.58187 10.487 0.001225 **
## Residuals 1699 94.265 0.05548
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.006134827
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$H185
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$H195 1 125710 125710 740.77 < 2.2e-16 ***
## Residuals 1719 291720 170
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.3011528
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$H185
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$HDiff 1 89689 89689 470.42 < 2.2e-16 ***
## Residuals 1719 327741 191
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.2148603
## `geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
## Warning: Removed 90 rows containing non-finite values (stat_smooth).
## Warning: Removed 90 rows containing missing values (geom_point).
## Analysis of Variance Table
##
## Response: F1$H185
## Df Sum Sq Mean Sq F value Pr(>F)
## F1$HDiff 1 89689 89689 470.42 < 2.2e-16 ***
## Residuals 1719 327741 191
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## [1] 0.2148603